[English] 日本語
Yorodumi
- PDB-1lpv: DROSOPHILA MELANOGASTER DOUBLESEX (DSX), NMR, 18 STRUCTURES -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1lpv
TitleDROSOPHILA MELANOGASTER DOUBLESEX (DSX), NMR, 18 STRUCTURES
ComponentsDoublesex protein
KeywordsTRANSCRIPTION / DROSOPHILA MELANOGASTER / DNA BINDING / GENE REGULATION
Function / homology
Function and homology information


imaginal disc-derived male genitalia development / male analia development / female analia development / female sex differentiation / sex-specific pigmentation / female somatic sex determination / imaginal disc-derived female genitalia development / sex comb development / somatic sex determination / negative regulation of developmental pigmentation ...imaginal disc-derived male genitalia development / male analia development / female analia development / female sex differentiation / sex-specific pigmentation / female somatic sex determination / imaginal disc-derived female genitalia development / sex comb development / somatic sex determination / negative regulation of developmental pigmentation / genital disc development / male sex differentiation / courtship behavior / male courtship behavior, veined wing generated song production / male courtship behavior / sex determination / sex differentiation / axon midline choice point recognition / RNA polymerase II transcription regulatory region sequence-specific DNA binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleus
Similarity search - Function
cysteine-rich DNA binding domain (DM domain) / DM DNA-binding domain / Doublesex dimerisation / Doublesex dimerisation domain / Doublesex dimerisation domain / DM DNA-binding domain / DMRT family / DM DNA-binding domain superfamily / DM DNA binding domain / DM DNA-binding domain signature. ...cysteine-rich DNA binding domain (DM domain) / DM DNA-binding domain / Doublesex dimerisation / Doublesex dimerisation domain / Doublesex dimerisation domain / DM DNA-binding domain / DMRT family / DM DNA-binding domain superfamily / DM DNA binding domain / DM DNA-binding domain signature. / DM DNA-binding domain profile. / Doublesex DNA-binding motif / Few Secondary Structures / Irregular
Similarity search - Domain/homology
MethodSOLUTION NMR / DISTANCE GEOMETRY, SIMULATED ANNEALING
AuthorsZhu, L. / Wilken, J. / Phillips, N. / Narendra, U. / Chan, G. / Stratton, S. / Kent, S. / Weiss, M.A.
Citation
Journal: Genes Dev. / Year: 2000
Title: Sexual dimorphism in diverse metazoans is regulated by a novel class of intertwined zinc fingers.
Authors: Zhu, L. / Wilken, J. / Phillips, N.B. / Narendra, U. / Chan, G. / Stratton, S.M. / Kent, S.B. / Weiss, M.A.
#1: Journal: Embo J. / Year: 1993
Title: The Drosophila Doublesex Proteins Share a Novel Zin Finger Related DNA-Binding Domain
Authors: Erdman, S.E. / Burtis, K.C.
#2: Journal: Nature / Year: 1998
Title: Evidence for Evolutionary Conservation of Sex-Determining Genes
Authors: Raymond, C.S. / Shamu, C.E. / Shen, M.M. / Seifert, K.J. / Hirsch, B. / Hodgkin, J. / Zarkower, D.
History
DepositionMay 8, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Doublesex protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,2563
Polymers6,1251
Non-polymers1312
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)18 / 40structures with the lowest energy
Representative

-
Components

#1: Protein Doublesex protein


Mass: 6125.327 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The sequence naturally occurs in Drosophila melanogaster (Fruit fly).
References: UniProt: P23023
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D TOCSY
121NOESY
131COSY
NMR detailsText: NMR EXPERIMENTS WERE CONDUCTED ON VARIAN INOVA 600 MHZ SPECTROMETERS. SOFTWARE VNMR5.1 AND FELIX WERE USED TO PROCESS NMR DATA. STRUCTURE DETERMINATION WAS PERFORMED ON A SILICON GRAPHICS WORK ...Text: NMR EXPERIMENTS WERE CONDUCTED ON VARIAN INOVA 600 MHZ SPECTROMETERS. SOFTWARE VNMR5.1 AND FELIX WERE USED TO PROCESS NMR DATA. STRUCTURE DETERMINATION WAS PERFORMED ON A SILICON GRAPHICS WORK STATION. IN 50 MM DEUTERATED TRIS, 10 MM DEUTERATED DTT.

-
Sample preparation

Sample conditionspH: 6.5 / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
X-PLORBRUNGERrefinement
VNMR5.1structure solution
RefinementMethod: DISTANCE GEOMETRY, SIMULATED ANNEALING / Software ordinal: 1
Details: MOLECULAR MODELS WERE OBTAINED BY DGII IMPLEMENTED IN INSIGHT II (BIOSYM INC., SAN DIEGO, CA), FOLLOWED BY REFINEMENT WITH SIMULATED ANNEALING IN X-PLOR (T.F.HAVEL, A.T.BRUNGER). RESIDUE 1 ...Details: MOLECULAR MODELS WERE OBTAINED BY DGII IMPLEMENTED IN INSIGHT II (BIOSYM INC., SAN DIEGO, CA), FOLLOWED BY REFINEMENT WITH SIMULATED ANNEALING IN X-PLOR (T.F.HAVEL, A.T.BRUNGER). RESIDUE 1 IN RESTRAINTS CORRESPONDS TO RESIDUE 35 IN DSX. TWO ZINC BINDING SITES ARE: C44,C47,H59,C63 AND H50,C68 C70, C73 EACH IN A TETRAHEDRAL PATTERN. (i.e., 10,13,25,29 and 16,34,36,39 in the coordinates). RESIDUE 35-40 AND 82-105 IN DEX ARE DISORDERED. Structures are giving for residues 35 to 86, corresponding to 1 to 52 numbered in the coordinates. NO MINOR CONFORMERS WERE DETECTED.
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 40 / Conformers submitted total number: 18

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more